The two men have been identified Cesar Santana and Leiner Miranda Lopez.
Santana is in custody. He was found and arrested Thursday night in Miami. Police say he was in a motel along Biscayne Boulevard.
Lopez has not been found. Both men are charged with desecrating and concealing human remains. Authorities say an autopsy shows Hernandez died from blunt force trauma to the head and compressions to the neck.
Hudson County prosecutors say the two men became persons of interest after they were pulled over as part of a traffic stop in Kearny on Sunday, a day before Hernandez was reported missing.
The 33-year-old mother of three and kindergarten teacher was last seen alive on Sunday. Her body was discovered Wednesday evening at a shallow grave in Kearny.
News 12 spoke with the family Thursday night and said Hernandez was living in a Jersey City home with the father of their three children. The family says they have been separated since November of last year. Their home is now a crime scene. People have stopped by to pay their respects with balloons, candles, and flowers.
"It's sad because her three kids are going to grow up without a mom. They still have no clue as to why this happened," said Sophie, a resident of Jersey City.
Hernandez's sister Jenny Taveras told News 12 she believes the father of their three children is the person responsible of her death. But there is no word from officials if that's who they have in custody.
A former neighbor and long-term friend, Jose Luna said, “We lost a beautiful person, a beautiful teacher, sister, daughter. You’d never hear anything bad from her mouth. She was always smiling…. I hope that animal pays for what he did. I won't call him anything better than an animal.”
Santana is being held in Florida and awaiting extradition.